Stefan; I made a thread about this issue here:
http://electro-music.com/forum/viewtopic.php?t=31032 . Kassen suggested that I send an email here, thinking that this might require some insight into RTAudio (not sure myself what it is).
That's the library for sound in& out that we use. It's cross-platform and supports different interfaces on those platforms. My reason for suggesting it was the strange thing that happened when you switched to multiple channels with your "main" outputs no longer carrying the signal. To me that's quite strange but I can't say whether that might be related to your real issue. It's hard to identify what exactly is going wrong from your audio file, it's a very weird sort of distortion but doesn't sound like plain clipping to me; the sound seems too dynamic for that. Yours, Kas.